Early in the antiquity, there was definite division of labor and specialized knowledge and skills for different fields. However, in terms of the knowledge related to human beings themselves, the situation was different. Under the influence of the idea that things could be understood by means of making comparison according to their structures if they are near and according to their shapes if they are far away, the sages in ancient times believed that the heaven and the earth have formed a big universe while the human body itself has constructed a small universe.

The big universe and the small universe communicate and interact with each other. The idea in the Daoism that all things must accord with the natural world was also based on the comparison between all things on the earth and the big universe in terms of their origination, development and death. In Huang Di Nei Jing (Yellow Emperor's Canon on Medicine), the idea of cultivating health in the four seasons was undoubtedly influenced by the theory of Daoism. According to the idea of cultivating health in the four seasons, all things begin to sprout in spring, grow in summer, ripen in autumn and store up in winter.

Such an analogy was used quite often in the medical books compiled in different dynasties in Chinese history, especially in establishing the theory and developing the therapeutic methods of TCM. Awareness of analogy used in TCM is the key to understand TCM.

In the theory of zang xiang (visceral and their manifestations, i.e. the heart is a monarch-like organ, the spleen is an granary-like organ, the liver is a general-like organ, the gallbladder is a judge-like organ), for example, the functions of the viscera are compared to the system of court. In the composition of a formula, the herbs used are categorized into four groups, monarch, minister, assistant and guide. In the theory of Channels and Collaterals, the circulation of the blood and qi is compared to the flow of water in the rivers and lakes in the natural world. In pathology and diagnostics, it is believed that there must be an extra space inside the body when pathogenic factors invade the body.

The way to remove pathogenic factors out of the body is to take measures to fill up this extra space. The therapeutic method for strengthening the healthy-qi and cultivating the primordial-qi and the therapeutic method for expelling pathogenic factors were just developed on the basis of such an idea. Diseases troubling human beings were compared to the flooding due to blockage of the rivers with silt. That was how the theory and methods for relieving stagnation and promoting digestion were developed. In pathology, chen xiang (ligmum aquilariae resinatum) was believed to be able to guide the blood and qi to flow downwards because it would not float when put into water. However flowers were thought to be able to direct the blood and qi to flow upwards because they grew on the top of the plants. In fact, many ideas in TCM concerning the cause and effect can be explained by analogy.

In ancient times, doctors summarized their way to analogize different things in thinking in such a way that doctors perceived by intuition and sense. The mystery of TCM theory, the flexibility of therapeutic methods and the perception of doctors all can be explained by analogy. In other words, the charm in TCM is just conceived in such a perceivable but inexpressible sense. Liang Qichao, a great scholar in the period of modern times (1873-1929) said: "The mystery of perceivable but inexpressible sense can be found in all fields of Chinese studies. Such a mysterious sense obviously hinders the enlargement of knowledge." The example taken by Liang was TCM. Compared with other studies and technologies in ancient Chinese science (such as astronomy and mathematics), TCM, undoubtedly, demonstrates many more features of traditional Chinese culture.

Today, the concept of conceivable but inexpressible but in sense permeating through the theory of TCM, which incompatible with modem science, is naturally questioned again and again by those who tend to evaluate traditional Chinese science, including TCM, according to the criteria and value of Western science.

Analogical thinking was frequently described in classic Chinese philosophy as interaction in the idea of "integration of the heavens and human beings". It is generally accepted in the academic fields as one of the basic ways of Chinese people's thinking, especially the idea of interaction between the heavens and human beings which is an important part in the framework of Chinese people's thinking. In the book entitled Li Shi Chun Qiu (Li Shi's Analects of History) compiled in the Qin and Han Dynasties, it says: "Things of the same group contract each other, qi of the same kind merges into each other and sounds of the same category respond to each other."

In the Northern Song Dynasty, Zan Ning (919-1001), by reviewing the studies made by people before him, compiled a book entitled Wu Lei Xiang Gan Zhi (Compendium of Interaction Between Different Things), listing 500 kinds of responses between different things. Cheng Yi (1033-1107), an important philosopher in the Northern Song Dynasty, deduced these phenomena into-a basic principle. That is "there is just one sense and one response in the universe." These analyses show that, apart from recognition of the empirical knowledge of TCM, one has to be aware of the great importance of interaction (or analogical thinking) in TCM.

The thinking way based on interaction and response is of dual nature, leading to either sorcery or science. Take harelip for example. The idea that harelip is caused by seeing a hare or eating hare meat during pregnancy was obviously generalized from witch taboo. However, the knowledge about fetal education accumulated in ancient times based on such a sort of thinking is now found to contain much scientific content.

Li Shizhen (1518-1593), a great doctor in the Ming Dynasty, also made use of such empirical knowledge of using herbs in his great book Ben Cao Gang Mu (Great Compendium of Materia Medica). For example, the weapon called tong qi, a firearm in ancient times, was used to deal with dystocia because it could shoot. Comb was used to deal with agalactia because it could comb hair. The former practice is certainly useless. But the latter one is certainly effective because to comb the breast around for hundreds of times means to massage the breast, quite similar to physical treatment.